DIA-based proteome profiling with PRM verification reveals the involvement of ER-associated protein processing in pollen abortion in Ogura CMS cabbage

Abstract

Ogura cytoplasmic male sterility (Ogura CMS) is extensively applied in hybrid seed production in cruciferous crops. However, the post-transcriptional molecular basis of Ogura CMS in cruciferous crops remains elusive. Here, a data-independent acquisition-based proteomic approach coupled with a parallel reaction monitoring-based targeted proteomic assay was used to analyze the proteome dynamics of Ogura CMS cabbage line RM and its maintainer line RF during floral bud development to obtain insights into the mechanism underlying Ogura CMS in cruciferous crops. A total of 9 162 proteins corresponding to 61 464 peptides were identified in RM and RF floral buds. The proteomic fluctuation of RM was weaker than that of RF. Differences in protein expression between RM and RF gradually enlarged with floral bud development. Fifteen continually up-regulated and eight continually down-regulated proteins were found in RM relative to RF throughout floral bud development. Differentially expressed proteins between RM and RF during floral bud development were implicated in the endoplasmic reticulum (ER)-associated protein processing pathway, in which most of them exhibited down-regulated expression in RM. These data suggest that ER-associated protein processing may be involved in pollen abortion in Ogura CMS cabbage by inhibiting the expression of critical factors. Our findings not only deepen the understanding of the molecular mechanisms of Ogura CMS in cruciferous crops but also provide better guidance for applying Ogura CMS in the hybrid breeding of cruciferous crops.